Hello,
If I understand correctly, you can change that last line to:
rownames(cancerAssays[['microRNA']]) = gsub('*', 'star', problematicNames, fixed = TRUE)
This approach worked for me when running the example provided in the MultiAssayExperiment reference manual (under the "MultiAssayExperiment" tab) to produce a basic object, then attempting to change the rownames of one assay. I've provided my exact code at the bottom of this message if you're interested or can't reproduce the solution I've provided.
Best,
-Nick
P.S. I'm learning to help others
library('MultiAssayExperiment')
library('sessioninfo')
example("ExperimentList")
exprmap <- data.frame(primary = c("Jack", "Jill", "Barbara", "Bob"),colname = c("array1", "array2", "array3", "array4"),stringsAsFactors = FALSE)
methylmap <- data.frame(primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),stringsAsFactors = FALSE)
rnamap <- data.frame(primary = c("Jack", "Jill", "Bob", "Barbara"),colname = c("samparray1", "samparray2", "samparray3", "samparray4"),stringsAsFactors = FALSE)
gistmap <- data.frame(primary = c("Jack", "Bob", "Jill"),colname = c("samp0", "samp1", "samp2"),stringsAsFactors = FALSE)
## Combine as a named list and convert to a DataFrame
maplist <- list(Affy = exprmap, Methyl450k = methylmap,RNASeqGene = rnamap, GISTIC = gistmap)
## Create a sampleMap
sampMap <- listToMap(maplist)
## Create an example phenotype data
colDat <- data.frame(sex = c("M", "F", "M", "F"), age = 38:41,row.names = c("Jack", "Jill", "Bob", "Barbara"))
## Create a MultiAssayExperiment instance
mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat,sampleMap = sampMap)
## Just to show what this object looks like now
mae
#A MultiAssayExperiment object of 4 listed
# experiments with user-defined names and respective classes.
# Containing an ExperimentList class object of length 4:
# [1] Affy: SummarizedExperiment with 5 rows and 4 columns
# [2] Methyl450k: matrix with 5 rows and 5 columns
# [3] RNASeqGene: matrix with 5 rows and 4 columns
# [4] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns
#Features:
# experiments() - obtain the ExperimentList instance
# colData() - the primary/phenotype DFrame
# sampleMap() - the sample availability DFrame
# `$`, `[`, `[[` - extract colData columns, subset, or experiment
# *Format() - convert into a long or wide DFrame
# assays() - convert ExperimentList to a SimpleList of matrices
## As a test, simply rename the rows of the "Affy" assay with integer values
rownames(mae[['Affy']]) = as.character(1:5)
## Check that the rownames are actually changed
assay(mae, 'Affy')
# array1 array2 array3 array4
#1 101 106 111 116
#2 102 107 112 117
#3 103 108 113 118
#4 104 109 114 119
#5 105 110 115 120
## Reproducibility info
session_info()
#─ Session info ───────────────────────────────────────────────────────────────
# setting value
# version R version 4.0.2 Patched (2020-06-24 r78746)
# os CentOS Linux 7 (Core)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2020-10-28
#
#─ Packages ───────────────────────────────────────────────────────────────────
# package * version date lib source
# assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.0.0)
# Biobase * 2.48.0 2020-04-27 [2] Bioconductor
# BiocGenerics * 0.34.0 2020-04-27 [2] Bioconductor
# bitops 1.0-6 2013-08-17 [2] CRAN (R 4.0.0)
# cli 2.1.0 2020-10-12 [2] CRAN (R 4.0.2)
# crayon 1.3.4 2017-09-16 [2] CRAN (R 4.0.0)
# DelayedArray * 0.14.1 2020-07-14 [2] Bioconductor
# fansi 0.4.1 2020-01-08 [2] CRAN (R 4.0.0)
# GenomeInfoDb * 1.24.2 2020-06-15 [2] Bioconductor
# GenomeInfoDbData 1.2.3 2020-05-18 [2] Bioconductor
# GenomicRanges * 1.40.0 2020-04-27 [2] Bioconductor
# glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
# IRanges * 2.22.2 2020-05-21 [2] Bioconductor
# lattice 0.20-41 2020-04-02 [3] CRAN (R 4.0.2)
# Matrix 1.2-18 2019-11-27 [3] CRAN (R 4.0.2)
# matrixStats * 0.57.0 2020-09-25 [2] CRAN (R 4.0.2)
# MultiAssayExperiment * 1.14.0 2020-04-27 [1] Bioconductor
# RCurl 1.98-1.2 2020-04-18 [2] CRAN (R 4.0.0)
# S4Vectors * 0.26.1 2020-05-16 [2] Bioconductor
# sessioninfo * 1.1.1 2018-11-05 [2] CRAN (R 4.0.0)
# SummarizedExperiment * 1.18.2 2020-07-09 [2] Bioconductor
# withr 2.3.0 2020-09-22 [2] CRAN (R 4.0.2)
# XVector 0.28.0 2020-04-27 [2] Bioconductor
# zlibbioc 1.34.0 2020-04-27 [2] Bioconductor
#
#[1] /users/neagles/R/4.0
#[2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/R/4.0/lib64/R/site-library
#[3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/R/4.0/lib64/R/library
